R code for Table 4 > library(multcomp) > glhtpcr<-glht(glm1,mcp(kit="Tukey")) > summary(glhtpcr) Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = pcr ~ kit, family = "binomial") Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) DNeasy - Direct PCR == 0 7.679e+00 1.011e+00 7.598 <0.001 *** EZNA - Direct PCR == 0 5.436e+00 7.654e-01 7.102 <0.001 *** NucleoSpin - Direct PCR == 0 8.383e+00 1.233e+00 6.796 <0.001 *** QuickExtract - Direct PCR == 0 5.436e+00 7.654e-01 7.102 <0.001 *** EZNA - DNeasy == 0 -2.243e+00 7.654e-01 -2.930 0.0241 * NucleoSpin - DNeasy == 0 7.038e-01 1.233e+00 0.571 0.9765 QuickExtract - DNeasy == 0 -2.243e+00 7.654e-01 -2.930 0.0243 * NucleoSpin - EZNA == 0 2.946e+00 1.042e+00 2.828 0.0327 * QuickExtract - EZNA == 0 -5.684e-14 3.877e-01 0.000 1.0000 QuickExtract - NucleoSpin == 0 -2.946e+00 1.042e+00 -2.828 0.0328 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) > confint(glhtpcr) Simultaneous Confidence Intervals Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = pcr ~ kit, family = "binomial") Quantile = 2.6778 95% family-wise confidence level Linear Hypotheses: Estimate lwr upr DNeasy - Direct PCR == 0 7.679e+00 4.972e+00 1.039e+01 EZNA - Direct PCR == 0 5.436e+00 3.387e+00 7.486e+00 NucleoSpin - Direct PCR == 0 8.383e+00 5.080e+00 1.169e+01 QuickExtract - Direct PCR == 0 5.436e+00 3.387e+00 7.486e+00 EZNA - DNeasy == 0 -2.243e+00 -4.292e+00 -1.928e-01 NucleoSpin - DNeasy == 0 7.038e-01 -2.599e+00 4.007e+00 QuickExtract - DNeasy == 0 -2.243e+00 -4.292e+00 -1.928e-01 NucleoSpin - EZNA == 0 2.946e+00 1.561e-01 5.737e+00 QuickExtract - EZNA == 0 -5.684e-14 -1.038e+00 1.038e+00 QuickExtract - NucleoSpin == 0 -2.946e+00 -5.737e+00 -1.561e-01 > glm2<-with(success,glm(sequence~kit,'binomial')) > summary(glm2) Call: glm(formula = sequence ~ kit, family = "binomial") Deviance Residuals: Min 1Q Median 3Q Max -0.9934 -0.8178 -0.6280 -0.2063 2.7788 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -3.8395 0.7146 -5.373 7.76e-08 *** kitDNeasy 2.9158 0.7500 3.888 0.000101 *** kitEZNA 2.3160 0.7631 3.035 0.002407 ** kitNucleoSpin 3.3899 0.7450 4.550 5.35e-06 *** kitQuickExtract 3.3005 0.7456 4.426 9.58e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 532.56 on 474 degrees of freedom Residual deviance: 474.13 on 470 degrees of freedom AIC: 484.13 Number of Fisher Scoring iterations: 6 > glhtseq<-glht(glm2,mcp(kit="Tukey")) > summary(glhtseq) Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = sequence ~ kit, family = "binomial") Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) DNeasy - Direct PCR == 0 2.91578 0.74997 3.888 <0.001 *** EZNA - Direct PCR == 0 2.31596 0.76312 3.035 0.0178 * NucleoSpin - Direct PCR == 0 3.38993 0.74497 4.550 <0.001 *** QuickExtract - Direct PCR == 0 3.30046 0.74562 4.426 <0.001 *** EZNA - DNeasy == 0 -0.59982 0.35126 -1.708 0.4071 NucleoSpin - DNeasy == 0 0.47415 0.30986 1.530 0.5209 QuickExtract - DNeasy == 0 0.38467 0.31142 1.235 0.7137 NucleoSpin - EZNA == 0 1.07397 0.34046 3.154 0.0123 * QuickExtract - EZNA == 0 0.98450 0.34188 2.880 0.0289 * QuickExtract - NucleoSpin == 0 -0.08947 0.29918 -0.299 0.9981 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) > confint(glhtseq) Simultaneous Confidence Intervals Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = sequence ~ kit, family = "binomial") Quantile = 2.6874 95% family-wise confidence level Linear Hypotheses: Estimate lwr upr DNeasy - Direct PCR == 0 2.91578 0.90031 4.93125 EZNA - Direct PCR == 0 2.31596 0.26514 4.36678 NucleoSpin - Direct PCR == 0 3.38993 1.38789 5.39196 QuickExtract - Direct PCR == 0 3.30046 1.29667 5.30424 EZNA - DNeasy == 0 -0.59982 -1.54382 0.34417 NucleoSpin - DNeasy == 0 0.47415 -0.35857 1.30686 QuickExtract - DNeasy == 0 0.38467 -0.45223 1.22158 NucleoSpin - EZNA == 0 1.07397 0.15902 1.98892 QuickExtract - EZNA == 0 0.98450 0.06573 1.90327 QuickExtract - NucleoSpin == 0 -0.08947 -0.89348 0.71454 > glm3<-with(success,glm(target~kit,'binomial')) > summary(glm3) Call: glm(formula = target ~ kit, family = "binomial") Deviance Residuals: Min 1Q Median 3Q Max -0.6280 -0.5647 -0.5197 -0.1455 3.0179 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) -4.543 1.005 -4.519 6.2e-06 *** kitDNeasy 3.020 1.040 2.903 0.0037 ** kitEZNA 1.419 1.128 1.258 0.2083 kitNucleoSpin 2.788 1.046 2.665 0.0077 ** kitQuickExtract 2.609 1.052 2.481 0.0131 * --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Dispersion parameter for binomial family taken to be 1) Null deviance: 311.02 on 474 degrees of freedom Residual deviance: 285.04 on 470 degrees of freedom AIC: 295.04 Number of Fisher Scoring iterations: 7 > glhttar<-glht(glm3,mcp(kit="Tukey")) > summary(glhttar) Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = target ~ kit, family = "binomial") Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) DNeasy - Direct PCR == 0 3.0198 1.0403 2.903 0.0263 * EZNA - Direct PCR == 0 1.4187 1.1277 1.258 0.6961 NucleoSpin - Direct PCR == 0 2.7879 1.0461 2.665 0.0522 . QuickExtract - Direct PCR == 0 2.6094 1.0517 2.481 0.0844 . EZNA - DNeasy == 0 -1.6011 0.5767 -2.776 0.0383 * NucleoSpin - DNeasy == 0 -0.2319 0.3942 -0.588 0.9743 QuickExtract - DNeasy == 0 -0.4104 0.4087 -1.004 0.8404 NucleoSpin - EZNA == 0 1.3692 0.5872 2.332 0.1209 QuickExtract - EZNA == 0 1.1906 0.5970 1.994 0.2470 QuickExtract - NucleoSpin == 0 -0.1785 0.4233 -0.422 0.9926 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 (Adjusted p values reported -- single-step method) > confint(glhttar) Simultaneous Confidence Intervals Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = target ~ kit, family = "binomial") Quantile = 2.68 95% family-wise confidence level Linear Hypotheses: Estimate lwr upr DNeasy - Direct PCR == 0 3.01980 0.23172 5.80788 EZNA - Direct PCR == 0 1.41873 -1.60341 4.44087 NucleoSpin - Direct PCR == 0 2.78790 -0.01576 5.59156 QuickExtract - Direct PCR == 0 2.60936 -0.20913 5.42785 EZNA - DNeasy == 0 -1.60107 -3.14675 -0.05539 NucleoSpin - DNeasy == 0 -0.23190 -1.28844 0.82465 QuickExtract - DNeasy == 0 -0.41044 -1.50573 0.68485 NucleoSpin - EZNA == 0 1.36917 -0.20444 2.94278 QuickExtract - EZNA == 0 1.19063 -0.40925 2.79051 QuickExtract - NucleoSpin == 0 -0.17854 -1.31291 0.95582